In 1122 Muiden was, together with Utrecht, granted some city rights by Emperor Henry V. After the lands around Muiden were given to Count Floris V, he began building Muider Castle at the mouth of the Vecht river. Muiden once again received city rights in 1296.

In 1673 the sea lock in the Vecht river was relocated from Fort Hinderdam to Muiden and in 1676 it was expanded with a sea wall along the Vecht mouth to prevent flooding.

The first defensive works date from the first half of the 15th century. In 1590 the walls are replaced with earthen mounds with bastions after a design by Adriaen Anthonisz. Muiden was the northern end of the Dutch Water Line.

Developments in warfare during the Franco-Prussian War of 1870 prompted another round of upgrades and the construction of forts part of the Stelling van Amsterdam, which includes the Muizenfort, the barracks on the Vestingplein, and the casemates in the ravelins. The layout of the fortification wall was revised.

In 1702 the hazardous production of gunpowder was removed from the city of Amsterdam. The vroedschap of Muiden granted a permit to Reinier van Cuyk of Amsterdam to build a gunpowder mill just west of Muiden that same year.

The factory flourished during the First World War, was liquidated in 1919, and was restarted in 1922. During the 20th century its production steadily increased and the town grew towards the factory. In 1972 it was renamed "Muiden Chemie". In the 1980s, it was accused of illegal shipments to Iran. In 1990 Muiden Chemie went bankrupt and was taken over by Britse Royal Ordnance, part of British Aerospace. After a fire in 2001 and ongoing concerns over safety, it was decided to close the factory permanently.